wavClusteR

DOI: 10.18129/B9.bioc.wavClusteR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see wavClusteR.

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Bioconductor version: 3.13

The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

Author: Federico Comoglio and Cem Sievers

Maintainer: Federico Comoglio <federico.comoglio at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("wavClusteR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("wavClusteR")

 

HTML	R Script	wavClusteR: a workflow for PAR-CLIP data analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, ImmunoOncology, RIPSeq, RNASeq, Sequencing, Software, Technology
Version	2.26.0
In Bioconductor since	BioC 3.0 (R-3.1) (7 years)
License	GPL-2
Depends	R (>= 3.2), GenomicRanges(>= 1.31.8), Rsamtools
Imports	methods, BiocGenerics, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), Biostrings(>= 2.47.6), foreach, GenomicFeatures(>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer(>= 1.39.7), seqinr, stringr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances	doMC
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	wavClusteR_2.26.0.tar.gz
Windows Binary	wavClusteR_2.26.0.zip
macOS 10.13 (High Sierra)	wavClusteR_2.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/wavClusteR
Source Repository (Developer Access)	git clone [email protected]:packages/wavClusteR
Package Short Url	https://bioconductor.org/packages/wavClusteR/
Package Downloads Report	Download Stats